Research workbench
Crystal structure of human beta-secretase in complex with nvp-ARV999
Analyse Crystal structure of human beta-secretase in complex with nvp-ARV999 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DV1
- Type
- protein
- Length
- 1,136 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-secretase 1
- EC
- 3.4.23.46
- UniProt
- P56817
- Ligands
- AR9
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-secretase 1 (EC 3.4.23.46) | protein | 377 | 16% helix, 41% strand | P56817 |
| B | Beta-secretase 1 (EC 3.4.23.46) | protein | 378 | 14% helix, 40% strand | P56817 |
| C | Beta-secretase 1 (EC 3.4.23.46) | protein | 381 | 16% helix, 39% strand | P56817 |
Ligands and binding sites
- AR9 · (2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.75 | 0.79 | 104 | AR9 |
| 2 | 537 | 0.75 | 0.82 | 65 | AR9 |
| 3 | 497 | 0.72 | 0.81 | 69 | AR9 |
| 4 | 342 | 0.63 | 0.79 | 50 | empty |
| 5 | 67 | 0.46 | 0.83 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1047 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P56817
- Elsewhere: RCSB PDB 3DV1 · PDBe 3DV1 · UniProt P56817
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